rs748995403

Variant names:

• chr1-36088910-CGCAGCGGCGATGGCG-C
• NM_017825.3:c.15_29delGATGGCGGCAGCGGC

Your query was ambiguous. Multiple possible variants found:

• chr1-36088910-CGCAGCGGCGATGGCG-C
• chr1-36088910-CGCAGCGGCGATGGCG-CGCAGCGGCGATGGCGGCAGCGGCGATGGCG

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP3

The NM_017825.3(ADPRS):​c.15_29delGATGGCGGCAGCGGC​(p.Met6_Ala10del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000146 in 1,372,712 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000015 (0 hom.)
• Consequence: ADPRS NM_017825.3 disruptive_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.95

Genes affected

ADPRS (HGNC:21304): (ADP-ribosylserine hydrolase) This gene encodes a member of the ADP-ribosylglycohydrolase family. The encoded enzyme catalyzes the removal of ADP-ribose from ADP-ribosylated proteins. This enzyme localizes to the mitochondria, in addition to the nucleus and cytoplasm.[provided by RefSeq, Feb 2009]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP3: Nonframeshift variant in repetitive region in NM_017825.3

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADPRS	NM_017825.3	c.15_29delGATGGCGGCAGCGGC	p.Met6_Ala10del	disruptive_inframe_deletion	Exon 1 of 6	ENST00000373178.5	NP_060295.1
ADPRS	XM_011541636.3	c.-351_-337delGATGGCGGCAGCGGC		5_prime_UTR_variant	Exon 1 of 5		XP_011539938.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADPRS	ENST00000373178.5	c.15_29delGATGGCGGCAGCGGC	p.Met6_Ala10del	disruptive_inframe_deletion	Exon 1 of 6	1	NM_017825.3	ENSP00000362273.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000146 AC: 2 AN: 1372712 Hom.: 0 AF XY: 0.00000148 AC XY: 1 AN XY: 677646

Gnomad4 AFR exome AF: 0.0000345

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000127

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-36554511;